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Microkeeper vs Square Payroll: Which Payroll Software Is Better?


Disclosure: We may earn commissions if you shop through the links below.

Last Updated: May 22, 2025

Both Microkeeper and Square Payroll are leading payroll software solutions, but which one is better for you and your business?

Below we compare Microkeeper and Square Payroll across nearly 50 different data points to help you make find the right one.

 

Microkeeper vs Square Payroll Reviews

MicrokeeperSquare Payroll
Trustpilot Rating3.64.2
Number of Trustpilot Reviews964049
iPhone App Rating4.44.8
Number of iPhone App Reviews1115
Android App Rating03.8
Number of Android App Reviews02660

Microkeeper vs Square Payroll Pricing

MicrokeeperSquare Payroll
Free TrialYesn/a
Free Trial Length1 monthn/a
Cheapest Plan NamePayroll & STP onlyPay Contractors Only
Cheapest Plan Cost Per Month$28$n/a
Mid Priced Plan NameStandardn/a
Mid Priced Plan Cost Per Month$28$n/a
Top Plan NamePremiumPay Employees & Contractors
Top Plan Cost Per Month$150$41

Microkeeper vs Square Payroll Features

FeaturesMicrokeeperSquare Payroll
Target Business SizeEnterpriseSmall business
Unlimited Payrolls✘✔
Automated Tax Filing & Payments✘✔
E-sign I-9 & W-4✘✘
Live Customer Support✘✔
Third-Party Integrations✔✔
Ability To Manage Employee Benefits✔✔
Employee Access To Platform✔✔
Direct Deposit✔✔
Expense Reimbursement✘✘
Time Off Accrual✔✔
Pre-Tax Deductions✔✔
Wage Garnishment✔✔
Background Checks✘✘
Check Printing✔✔
Check Delivery✘✔
API✔✔

Microkeeper Payroll & STP only Features

  • Payroll Processing
  • Leave
  • Public Holidays
  • Super Calculations
  • Employee Self Service Console
  • Paperless Employee Onboarding
  • Internal Messaging
  • Employee File Storage
  • Custom Reports
  • Native Xero Integration
  • MYOB / Sage / … Integration
  • Single Touch Payroll Compliance
  • 9-5 Email Support
  • 9-5 Phone Support

Square Payroll Pay Contractors Only Features

  • We mail all 1099-NEC forms
  • M–F 6 a.m. to 6 p.m. PT support
  • Pay by check, direct deposit, or Cash App
  • Free seasonal inactivity
  • All features included, with no hidden fees
  • No commitment, cancel anytime

Microkeeper Premium Features

  • Payroll Processing
  • Leave
  • Automated Award Application
  • Public Holidays
  • Super Calculations
  • SMS Rosters
  • iCal, Google Calendar, Outlook Export
  • Push Notifications
  • Print Export
  • Roster Confirmation
  • AutoRoster (Automated Shift Sheduling)
  • Shift bidding
  • Facial Recognition
  • Fingerprint Clocking
  • NFC Tag Clocking
  • GPS Clocking On Smart Device
  • Timesheet Tick Approval
  • Timesheet vs Roster Comparison
  • Employee Self Service Console
  • Paperless Employee Onboarding
  • Internal Messaging
  • Employee File Storage
  • Skills Matrix
  • Custom Reports
  • Native Xero Integration
  • MYOB / Sage / … Integration
  • Single Touch Payroll Compliance
  • Super Clearing House
  • 9-5 Email Support
  • 9-5 Phone Support

Square Payroll Pay Employees & Contractors Features

  • No additional fees
  • Full-service payroll
  • Payroll for employees and contractors
  • Automatic payroll tax calculations
  • All tax filings and payments
  • Multistate payroll
  • Live support for account setup
  • Timecards and employee app
  • Track and import tips and commissions
  • We mail W-2s and 1099-NEC forms
  • Pay by check, direct deposit, or Cash App
  • M–F 6 a.m. to 6 p.m. PT support
  • No commitment, cancel anytime
  • Unlimited pay runs per month
  • Free seasonal inactivity

Microkeeper vs Square Payroll Pro & Cons

MicrokeeperSquare Payroll
Pros
  • 100% Australia Focused
  • Good UX
  • Great tech support
  • Budget-friendly (only for payroll only and standard packages)
  • Updates and information about governmental requirements
  • All-in-one solution
  • Mobile App
  • Self Service
  • User Friendly
Cons
  • Reporting could use significant improvement
  • Integration with platforms such as MYOB isn’t seamless and is prone to error
  • Limited employee dashboard
  • Pricey premium package that only seems to be targeting big businesses
  • Starter plan is pretty useless
  • Not User Friendly
  • Room for Improvement
  • Slow

Other Payroll Software Comparisons

  • Justworks vs PayCaptain
  • PrimePay vs Justworks
  • Paylocity vs Hourly
  • OnPay vs CheckMark Payroll
  • HRONE vs Push Payroll
  • Namely vs Kashflow Payroll
  • QuickBooks Payroll vs Online Paystub Generator
  • Plane vs Keka
  • Patriot Software vs Fingercheck
  • SurePayroll vs CloudPay

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